1KCD - JenaLib

Title :   ENDOPOLYGALACTURONASE I FROM STEREUM PURPUREUM COMPLEXED WITH TWO GALACTURONATE AT 1.15 A RESOLUTION.

Authors :   T. Shimizu, T. Nakatsu, K. Miyairi, T. Okuno, H. Kato

Date :   08 Nov 01 (Deposition) - 05 Jun 02 (Release) - 14 Oct 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.15

Chains :   Asym./Biol. Unit : A

Keywords :   Beta Helical Structure, Glycoside Hydrolase, Silver-Leaf Inducing Substance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Shimizu, T. Nakatsu, K. Miyairi, T. Okuno, H. Kato
Active-Site Architecture Of Endopolygalacturonase I From Stereum Purpureum Revealed By Crystal Structures In Native And Ligand-Bound Forms At Atomic Resolution.
Biochemistry V. 41 6651 2002
PubMed-ID: 12022868 | Reference-DOI: 10.1021/BI025541A
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:120 , ASN A:151 , ASP A:153 , ASP A:173 , ASP A:174 , GLY A:200 , SER A:201 , LYS A:228 , TYR A:262 , GTR A:1002 , HOH A:2033 , HOH A:2036 , HOH A:2059 , HOH A:2115 , HOH A:2235 , HOH A:2256 , HOH A:2283 , HOH A:2284 , HOH A:2285 , HOH A:2286 , HOH A:2287 , HOH A:2438	BINDING SITE FOR RESIDUE GTK A 1001
2	AC2	SOFTWARE	ASN A:91 , HIS A:150 , ASN A:151 , ASP A:173 , HIS A:195 , ARG A:226 , LYS A:228 , TYR A:262 , GTK A:1001 , HOH A:2055 , HOH A:2059 , HOH A:2110 , HOH A:2283 , HOH A:2396	BINDING SITE FOR RESIDUE GTR A 1002
3	AC3	SOFTWARE	ALA A:15 , GLY A:16 , ASN A:91 , ASN A:92 , HOH A:2180 , HOH A:2521	BINDING SITE FOR RESIDUE NAG A 2001
4	AC4	SOFTWARE	ASN A:160 , ASN A:161 , ASN A:182 , HOH A:2220 , HOH A:2437	BINDING SITE FOR RESIDUE NAG A 2002
5	AC5	SOFTWARE	GLY A:30 , THR A:55 , ASN A:308 , HOH A:2483	BINDING SITE FOR RESIDUE CL A 2003

SS Bonds (3, 3)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:333
 aligned with P79074_9AGAR | P79074 from UniProtKB/TrEMBL  Length:403

    Alignment length:333
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   
         P79074_9AGAR    27 CTVKSVDDAKDIAGCSAVTLNGFTVPAGNTLVLNPDKGATVTMAGDITFAKTTLDGPLFTIDGTGINFVGADHIFDGNGALYWDGKGTNNGTHKPHPFLKIKGSGTYKKFEVLNSPAQAISVGPTDAHLTLDGITVDDFAGDTKNLGHNTDGFDVSANNVTIQNCIVKNQDDCIAINDGNNIRFENNQCSGGHGISIGSIATGKHVSNVVIKGNTVTRSMYGVRIKAQRTATSASVSGVTYDANTISGIAKYGVLISQSYPDDVGNPGTGAPFSDVNFTGGATTIKVNNAATRVTVECGNCSGNWNWSQLTVTGGKAGTIKSDKAKITGGQYL 359
               SCOP domains d1kcda_ A: Polygalacturonase                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1kcdA00 A:3-335 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------Glyco_hydro_28-1kcdA01 A:17-331                                                                                                                                                                                                                                                                                            ---- Pfam domains
         Sec.struct. author .ee...hhhhhh....eeee..eee.....eee......eeee...eee.........eeeeeeeeeee....eee.hhhhh................eeeeeeeeee..eee......eeeeeeeeeeeee..eee.hhhhhhhh......eeee...eeee..eee.....eeeeeeeeeeee..eee....eeeeee....eeeeeeee..eeeeeeeeeeeeee......eeeeeeee..eeeeeeeeeeeeeeee............eeeeee....eeeee....eeeeee...ee.eee...eeee......ee....eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kcd A   3 CTVKSVDDAKDIAGCSAVTLNGFTVPAGNTLVLNPDKGATVTMAGDITFAKTTLDGPLFTIDGTGINFVGADHIFDGNGALYWDGKGTNNGTHKPHPFLKIKGSGTYKKFEVLNSPAQAISVGPTDAHLTLDGITVDDFAGDTKNLGHNTDGFDVSANNVTIQNCIVKNQDDCIAINDGNNIRFENNQCSGGHGISIGSIATGKHVSNVVIKGNTVTRSMYGVRIKAQRTATSASVSGVTYDANTISGIAKYGVLISQSYPDDVGNPGTGAPFSDVNFTGGATTIKVNNAATRVTVECGNCSGNWNWSQLTVTGGKAGTIKSDKAKITGGQYL 335
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (P79074_9AGAR | P79074)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0004650	polygalacturonase activity	Catalysis of the random hydrolysis of (1->4)-alpha-D-galactosiduronic linkages in pectate and other galacturonans.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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	Cis Peptide Bonds
		Gly A:125 - Pro A:126	[ RasMol ]
		Gly A:200 - Ser A:201	[ RasMol ]
		Gly A:58 - Pro A:59	[ RasMol ]
		His A:98 - Pro A:99	[ RasMol ]
		Tyr A:262 - Pro A:263	[ RasMol ]

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